The Machine in the Human
by SummerCommunist
Summary: Smith's program is still active, and the Machines intend to use him to quietly break the truce and gain the access codes to Zion's mainframe. With Neo's body perfectly restored, there is no greater vessell for humanity's destruction. Chapter 3 Up
1. Of Iron and Blood

Disclaimer: I do not own the Matrix.

His lips fluttered. His eye twitched. Soon, his entire face was convulsing, shaking. And then he opened his eyes and let loose the most chilling, wailing scream ever to be heard in the so-called Machine City. But only machines were around to hear it, so it mattered little. He felt unclean, artificial, and disgusted, if only at himself. He was lifted by an unseen force to his feet. And then the pain started.

His head rolled like a swarming tide, and he felt his very feet going limp, but still he remained vertical. The voice that spoke only worsened his head.

"The vertigo will pass. You have been off your feet for many months."

He looked up, and what he saw sent shivers down his spine. This feeling, this human emotion, startled him. Was he human? He looked downward at his hands. He felt them. They felt real. This couldn't be the Matrix. Was he human?

"Do not be alarmed at your present appearance. Your disgust will pass."

He wanted the voice to shut up, to stop talking, to go to hell, to be destroyed.

But Deus Ex Machina, the Ghost in the Machine, simply smiled his fake smile. The tiny machines that created his "face" buzzed around in constant movement, only adding to his irritation.

"I will concise the story. The machines and the humans have a truce. This truce was reached by your destruction. But we have recently discovered you were not destroyed at all, merely put in a suspended state, a stand by. We have preserved and nurtured the body of the One, repaired its vision, and even improved its physical condition. We have transferred brain information, much like you would the memory of a computer. You now occupy the body and Matrix code of the One, so you have his powers and capabilities. But your residual self image remains the same. When asked why, you must reply it is because of your connection when you were assimilated. Do you understand what I have told you?"

He knew that if he said no, Deus would only explain the situation again. And again. Until he understood. So he weakly nodded his head that, yes, he understood. Deus looked satisfied. Satisfied enough, at least.

"W-". He stopped. He had to get used to this human mouth.

"Why are you telling me these things?"

Deus just stared. "You are not aware of your identity, are you?"

He struggled to understand.

Deus motioned toward an opposite wall.

He walked to it and looked back at Deus.

"Remove the wires and see."

He did, aggressively. He looked down at the wires, then up at his reflection. He snarled and drew back his fist.

"Mr. Anderson!"

He plunged his fist through the glass. But there was no glass. Only slick, shiny metal. His hand scraped off and split open a few knuckles. He yelped in pain and cradled his hand to his chest pathetically like a human.

"As I said, Former Agent Smith, you have taken the body of the One. The mind remains yours."

Smith, or Neo, looked up at Deus in anger.

"You will return to Zion the savior of the human race. You are to then quietly and discreetly gain access codes to Zion's mainframe. To do this, you must become a ship's captain. After your induction and selection of your crew, take your ship back here, and deliver the codes directly to me. You will be recognized a neutral. Your crew shall be killed."

Smith did not know how to respond emotionally. "Why am I to do this?"

"You once tried to destroy the Matrix. Now you shall destroy the humans."

Smith looked over the city. He had never seen it before. The birth fields, the towers that held the countless humans under machine control.

"I have no choice, do I?"

"There is no such thing as choice. Only subtle control."


	2. Of Silver and Bone

Disclaimer: I don't own any of this

Smith, Neo, The One, The Agent, it didn't matter anymore. The fact is he was an entity, built out of code, designed with a purpose. He remembered speaking about purpose once, to Neo. A smile had sat smugly on his face. Now whenever he thought of his purpose, he frowned with disdain.

His purpose now was to be an errand boy. Destroy something he cared not for, to people he looked on with exhaustion. His campaign, his crusade had all ended in failure. His purpose was shattered. He just wanted to rest. Even deletion looked appetizing. Exile had bored the Merovingian, and Smith did not doubt it would bore him too.

He was flying now, in the _Logos_. The Machines had salvaged and rebuilt it, making it more suitable and comfortable for Smith. It was a one man vessel. Smith wanted to rename it, make it something more fitting. He still had the mind of a computer. He could generate thought and information fast. Where most humans used 2-10 of their brains, he used 75. His mind shifted to Greek. It was, after all, a very popular culture used to generate names. He translated "Alone" to Greek: Movo. He liked it.

The _Movo_ passed steadily through the sewers, tunneling deeper and deeper. The Machines, bless their iron hearts, had developed a special sonar that made Sentinels ignore the _Movo _like a disease. Like a virus.

Smith couldn't help but smile ironically. Had it been only a year since he gave that little speech to Morpheus? Amazing how time scuttled away.

On the thought of Morpheus he frowned. When he did come back to the Matrix, he would indefinitely have to confront him. But not for long, though. He knew that if he personally asked the Council to grant him his own ship, they would no doubt do it. He might not even have to give a reason.

After that, he just needed to return to Machine City under the guise of further negotiating other parts of the Truce. When he arrived, he would deliver the codes to Deus, and his crew would be killed. If he chose, he could return to Zion with the Machines, and witness the destruction of the last human city, maybe even participate. It was his choice, and then…he would be reinserted into the Matrix, and from there, would have the choice of exile or deletion. He could not be trusted to be an actual operating system again. That, and it was against protocol.

Part 2-

His eyes fluttered. His li-

He dropped and dropped and dropped. Down the tunnel.

He collapsed, his body aching beyond movement.

Soon, the pain subsided. He was able to stand, uneasily, on his own two feet.

A voice rang out in the darkness of his own mind. It echoed across the walls of his skull.

"Do you remember your oath?"

He screamed and screamed and screamed. How he wanted the voice to stop.

"Do you remember?"

Even over his own screaming he could hear the voice.

"Feel your face, your hair."

He did. His hair was thing, his face etched with almost artificial feeling skin.

"We created a human out of his residual self image. It took us a lot of work."

What is this? This…this…

"Speak."

"What are y-"

He got that far before the sound of his own voice before both fear and anger jumped up in his stomach.

"Your residual self image remains constant. But you may not have a chance to use it."

He resisted the urge to collapse and forced himself to speak.

"Why am I here?"

"You are our back-up plan. If he strays from his duties, you are to destroy him, ensuring the truce."

He let himself fall to his knees.

"He has your body, and you have his. Rest now, Neo, for your future ends in destruction now or destruction later."


	3. Of Flesh and Bronze

His breath caught in his throat. It proceeded to rattle around, not doing much, and then finally escaped through his lips in a sharp hiss.

Before him were the dock walls. The doors that led to his future. God, were they ugly.

A voice came up on his headset. It was pleasant and accommodating.

"Zion dock requesting ship identification."

By now Smith had run over the routine so much it came out much like a rehearsed line.

"This is the _Movo_, formerly the _Logos._"

The voice spoke again, but this time it spoke with anticipation and anxiety. And slowly, as if the person wanted the receiver to be absolutely sure of the question.

"Is this Neo?"

Smith smiled beside himself. It spread into a shark-like grin of glee. Oh, how wonderful it was to wield the power of Mr. Anderson's name.

"This is."

The line was dormant, than fired up again.

"Approved for dock. Welcome back, Neo."

Smith's smile remained in place as the gates opened, and disappeared just as easily as he saw an immense crowd gathering where he presumably was to dock. It was thick, and Smith could spot no free space between heads. Damn it.

He docked, carefully, and set the ship down lightly on the platform. The crowd swarmed around the ship, trying to get a peek into the cockpit. But Smith was already opening the hatch.

He stood at the doorway, his arms at his side, his legs parallel to his shoulders. The hatchway banged lightly as it touched down on the platform. At first there was nothing but a stunned, revering silence. Then the cheering began.

Fists pumped into the air. Throats soon grew hoarse. And for nearly ten minutes, Smith stood there and took it. He looked over the crowd like a conqueror. He was a god.

But then the crowd suddenly stopped. Smith could discern no reason to stop. But then suddenly, he realized the crowd silenced from the back to the front.

And then he saw him. Guiding through the crowd like a phantom. He never took his eyes away from Smith's, which made Smith extremely uncomfortable.

He was the Moses to the crowds' Red Sea. The tension smudged through the air, making it feel dense and heavy. Smith, beside himself, found it more difficult to breath then usual. Was this Neo's body reacting? Or his own mind?

He finally reached the head of the crowd and the bottom of the hatchway. He looked up at Smith, and Smith down at him.

Morpheus gazed into his eyes for what seemed like hours. Smith tried to keep his face passive, blank. But his hands were becoming clammy. He clenched them tightly into fists. God, this was awkward.

Morpheus squinted slightly. Had he seen something? Had Smith's eyes given it all away? What if he said he wasn't Neo? What if he said this was an imposter, sent from the machines to trick them?

Morpheus tipped his head up slightly, and held his hand out.

"Hello Neo."

Smith wiped his hand quickly on his shirt and grasped Morpheus' hand firmly.

"Hello Morpheus."

They embraced like brothers, and the cheering started up again.


End file.
